Ash's Shadow Pokemon Journey XD
by MegaHeracross214
Summary: Ash has to save the Orre Region again this time from Cipher's newest creation XD001 which is Shadow Yveltal, more Shadow Pokemon, and Cipher again. Part 3/5 sequel up.
1. HQ Lab & Cipher Lab

**i don't own Pokemon.**

Ash went through a portal created by Hoopa and he landed near the Pokemon HQ Lab and found an Eevee with no trainer so he captured him. He was challenged by Cipher Peon Naps his only Pokemon was a Shadow Cubchoo so Ash sent out his new Eevee and he managed to poison Cubchoo with Toxic and was snagged and purified him and he learned that Professor Krane was kidnapped. He had to go to Gateon Port where his Eevee wanted to evolve into Vaporeon so he got a Water Stone from a mannamed Kerr.

Eevee evolved into Vaporeon and when he went outside he was Casual Dude Cyle who sent out a Taillow who was defeated by Jolteon's Thunder Shock and the Shadow Shedinja so Ash sent Noctowl who put Shedinja to sleep with Hypnosis. The Bug/Ghost type was then snagged and purified.

On the top floor of the lighthouse he was challenged by Bodybuilder Kilen who sent out a Zubat and Shadow Poochyena while Ash sent out Girafarig and Vaporeon. Zubat was defeated by Vaporeon's Aurora Beam while Poochyena was snagged and purified after being paralyzed by Girafarig's Thunder Wave.

The next stop was the Cipher Lab. He was then challanged by Resix who sent out a Slugma and Shadow Litleo while Ash sent out Vaporeon and Dunsparce. Slugma fell to Vaporeon's Bubble Beam and Dunsparce paralyzed Litleo with Glare who was then snagged and purified.

Second was Blusix who sent out a Horsea and Goldeen who were defeated by Jolteon's Tunderbolt and Dedenne's Discharge respectively and then he sent out Shadow Spheal who was paralyzed by Dunsparce's Glare then was snagged and purified.

Third was Browsix who sent out a Hoothoot and the Shadow Baltoy while Ash sent out Gliscor and Abomasnow. Hoothoot was defeated by Gliscor's Stone Edge and Baltoy was put to sleep by Abomasnow's Grass Whistle. Baltoy was then snagged then purified.

Yellosix was next and sent out a Chinchou and an Electrike who fell to Torterra's Bulldoze and Whiscash's Mud Bomb. His last Pokémon was the Shadow Stunfisk who was immobilized by Beheeyem's Telekinesis. Stunfisk was then snagged and purified.

Fifth was Purpsix whose Grimer, Koffing, and Tentacool fell to Spiritomb's Psychic, Beheeyem's Psychic, and Sigilyph's Psychic. The Shadow Gulpin was snagged and purified after getting put to sleep by Gardevoir's Hypnosis.

Last was Greesix whose Lotad, Oddish, Cacnea, Shroomish, and Pineco fell Noctowl's Air Slash, Honchkrow's Fly, Torkoal's Heat Wave, Emboar's Heat Crash, and Magcargo's Flamethrower. While the Shadow Seedot who was snagged and purified after getting paralyzed by Sigilyph's Thunder Wave.

Inside he was challenged by Cipher Peon Nexir whose Swinub and Shuppet fell to Tauros' Rock Smash and Absol's Pursuit. The Shadow Mareanie was snagged then purified after getting levitated by Sigilyph's Telekinesis.

Next he was challenged by Cipher Peon Solox whose Ralts, Voltorb, and Bagon fell to Skarmory's Steel Wing, Stunfisk's Mud Bomb and Kommo-o's Clanging Scales. While the Shadow Numel was snagged and purified after getting restrained by Hariyama.

Third he was challenged by Cipher RD Coffy who sent out the Shadow Dustox and a Wingull. Ash sent out Numel and Jolteon. Numel burned Dustox with Will-O-Wisp and Ash snagged him while Jolteon defeated Wingull with Thunder Shock. Coffy's last Pokemon were a Pineco and Qwilfish. Ash returned Numel and Jolteon and sent out Litleo and Unown. Litleo defeated Pineco with Incinerate and Unown defeated Qwilfish with Hidden Power. Ash then returned his Pokemon and purified Dustox.

He was then challenged by Cipher Peon Cabol whose Magnemite, Psyduck, and Remoraid fell to Mamoswine's Mud Bomb, Lanturn's Thunderbolt, and Jolteon's Zap Cannon and Shadow Carvanha was snagged then purified after getting paralyzed by Raichu's Thunder Wave.

He then went to the Cave Poké Spot and caught a Nidoran F, a Shiny Zubat, and a Trapinch. He also fought Miror B. He defeated two of his Lombre with Scolipede's Poison Tail and Butterfree's Air Slash. His last two Pokémon are his third Lombre and the Shadow Voltorb. Mareanie's Poison Jab defeated Lombre and Beheeyem levitated Voltorb with Telekinesis. Ash then snagged and purified Voltorb.

He then traded the Trapinch for Duking's Machop.

The ONBS building was under attack by Cipher. The first one Ash was challenged by was Cipher Peon Torkin. The peon first sent out a Kecleon and a Surskit. In response Ash sent out Machop and Vesbiquen. Machop defeated Kecleon with Karate Chop and Vespiquen defeated Surskit with Aerial Ace. Torkin's last Pokémon was the Shadow Meinfoo so Ash returned Machop and Vespiquen and sent out Cofagrigus who used Telekinesis to levitate Meinfoo who was snagged and purified.

The second peon who challenged him was Cipher Peon Mesin who sent out a Spinarak and a Beautifly so Ash sent out Cofagrigus who defeated Spinarak with Psychic and Voltorb who defeated Beautifly with Thunderbolt. Mesin's lastly sent out a Dustox and the Shadow Vulpix so Ash returned Cofagrigus and Voltorb and sent out Machop and Noctowl. Machop defeated Dustox with Rock Tomb and evolved into Machoke while Noctowl put Vulpix to sleep with Hypnosis. Vulpix was then snagged and purified.

The second peon that challenged him was Cipher Peon Dilly who sent out a Gulpin and Mareep. Ash sent out Bruxish and Mudsdale. Bruxish defeated Gulpin with Psychic Fangs while Mudsdale defeated Mareep with High Horsepower. Dilly's last Pokemon were a Luvdisc and the Shadow Bellossom. Ash returned Bruxish and Mudsdale and sent out Lanturn and Vulpix. Luvdisc was defeated by Lanturn's Thunderbolt and Bellossom was burned by Vulpix's Will-O-Wisp. Then Ash snagged and purified Bellosom.

The third peon that challenged Ash was Cipher Peon Lobar who sent out a Sneasel and a Yanma. Ash sent out Sylveon and Armaldo. Sylveon defeated Sneasel with Draining Kiss and Armaldo defeated Yanma with Rock Blast. The last Pokémon that Lobar sent out were a Misdreavus and the Shadow Duskull so Ash returned Sylveon and Armaldo. Ash then sent out Yanmega who defeated Misdreavus with Shadow Ball and Altaria put Duskull to sleep with Sing. Ash then snagged and purified Duskull.

The last peon that challenged him was Cipher Peon Feldas who sent out a Kadabra and a Flaaffy so Ash sent out Weavile and Quagsire. Weavile defeated Kadabra with Night Slash and Quagsire defeated Flaaffy with Mud Bomb. Feldas' last Pokémon were a Vigoroth and the Shadow Ralts. Ash returned Weavile and Quagsire and sent out Machoke and Spiritomb. Machoke defeated Vigoroth with Brick Break while Ralts was put to sleep by a Hypnosis from Spiritomb and he snagged and purified Ralts.

Ash then challenged Cipher-Cmdr Exin whose first pair of Pokémon were a Loudred and a Girafarig so Ash sent out Meinfoo and Shedinja. Meinfoo defeated Loudred with Aura Sphere and Shedinja defeated Girafarig with Night Slash. Exin returned his fainted Pokémon and sent out a Raichu and the Shadow Mawile so Ash returned Meinfoo and Shedinja and sent out Baltoy and Magcargo. Baltoy defeated Raichu with Drill Run while Magcargo put Mawile to sleep with Yawn and Ash snagged and purified Mawile.


	2. Phenac, Key Lair, Citadark, Lighthouse

**I don't own Pokemon.**

The next stop was Phenac City where he was challenged by Cipher Peon Exinn whose Seviper, Golbat, and Mightyena fell to Girafarig's Psychic, Dedenne's Volt Switch, and Meinfoo's Focus Blast and the Shadow Bergmite held by Hariyama and was snagged and purified.

He was then challenged by Cipher Peon Gonrag whose Murkrow and Ariados who fell to Stunfisk's Thunderbolt and Litleo's Flamethrower while the Shadow Masquerain was paralyzed by Jolteon's Thunder Wave and then was snagged and purified.

Ash was challenged by Cipher Peon Pellim who sent out a Sudowoodo and the Shadow Clamperl. In response Ash sent out Tentacruel and Girafarig. Tentacruel defeated Sudowoodo with Scald and Girafarig paralyzed Clamperl with Thunder Wave. Ash then snagged and purified Clamperl.

Third he was challenged by Cipher Peon Greck whose Nuzleaf and Torkoal who fell to Ledian's Mach Punch and Blastoise's Water Pulse while the Shadow Vanillite put to sleep by Ralts' Hypnosis and was snagged and purified.

Fourth he was challenged by Cipher Peon Greesix who sent out a Lotad and Oddish. Ash responded to that with Dustox who defeated Lotad with Sludge Bomb and Masquerain who defeated Oddish with Air Slash. Next Greesix sent out a Cacnea and Shroomish. So Ash returned Dustox and Masquerain and sent out Furret and Toucannon. Furret defeated Cacnea with Fire Punch and Toucannon defeated Shroomish with Beak Blast. Greesix's last Pokemon were a Pineco and the Shadow Fomantis. Ash returned Furret and Toucannon and sent out Zubat who defeated Pineco with Brave Bird plus he evolved into Golbat and Numel who put Fomantis to sleep with Yawn. Fomantis was then snagged and purified.

Ash snagged and purified the Shadow Brionne, Salandit, Skrelp, Pom Pom Style Oriocorio, and Komala from the other Hexagon Brothers. He also snagged and purified the Shadow Spearow. All thanks to Beheeyem's Telekinesis.

He went to the Prestige Precept Gym and was challenged by Cipher Peon Eloin who sent out a Linoone and Roselia while Ash sent out Machoke and Snorlax. Machoke defeated Linoone with Cross Chop and Snorlax defeated Roselia with Ice Punch. Then Eloin sent out her last Pokémon which was the Shadow Natu. Ash then returned Machoke and Snorlax and sent out Vulpix who burned the Psychic/Flying type Tiny Bird Pokémon with Will-O-Wisp. Ash snagged and purified the Natu.

The second Cipher Peon he faced was Cipher Peon Fasin who sent out a Remoraid and Golbat. Ash sent out Octillery and Lapras. Octillery defeated Remoraid with Charge Beam while Golbat was defeated by Lapras' Ice Beam. Fasin's last Pokémon was the Shadow Roselia so Ash returned Octillery and Lapras and sent out Duskull. The Requiem Pokémon burned Roselia with Will-O-Wisp. Ash then snagged and purified Roselia.

Ash was then challenged by Cipher Peon Fostin who sent out a Kadabra and Sneasel so Ash sent out Ninjask and Staraptor. Ninjask defeated Kadabra with Fury Cutter while Sneasel fell to a Close Combat from Staraptor. Fostin's last Pokémon was the Shadow Meowth so Ash returned Ninjask and Staraptor and sent out Steelix. The Iron Snake Pokémon used Toxic to poison Meowth who was then snagged and purified.

He was then challenged by Cipher Peon Faltly who sent out a Chimecho and Stantler. In response Ash sent out Volcarona and Scrafty. Volcarona defeated Chimecho with Bug Buzz and Scrafty defeated Stantler with Head Smash. Faltly's last Pokémon was the Shadow Koffing. Ash returned Volcarona and Scrafty and sent out Cofagrigus who used Telekinesis on Koffing. Then Koffing snagged and purified

He was challenged next by Cipher Peon Egron who sent out a Hoothoot and Graveler so Ash sent out Gigalith and Steelix. Gigalith defeated Hoothoot with Smack Down and Steelix defeated Graveler with Dig. Egron's last Pokémon was the Shadow Seel so Ash returned Gigalith and Steelix and sent out Koffing. Koffing poisoned Seel with Poison Gas so Seel was snagged and purified.

The last member of Cipher in the area was Cipher Admin Snattle who sent out a Lanturn and Quagsire in response to that Ash sends out Torterra and Venusaur. Lanturn was defeated by Torterra's Giga Drain and Quagsire was defeated by Venusaur's Mega Drain. Snattle then sent out the Shadow Lunatone and a Castform so Ash returned Torterra and Venusaur. After that he sent out Hippowdon and Snorlax. Lunatone was put to sleep by Hippowdon's Yawn and was snagged and purified while Castform was defeated by a Brick Break from Snorlax. The Cipher Admin's last Pokémon was a Togetic. Ash returned Hippowdon and Snorlax and sent out Rampardos who defeated Togetic with Head Smash.

He went to Cipher Key Lair and challenged Thug Zook who sent out the Shadow Zangoose so Ash sent out Bellossom. Zangoose was paralyzed by Bellossom's Stun Spore. Ash then snagged and purified Zangoose.

He then went to the Rock Poke Spot and captured an Aron, Sandshrew, and Wooper who he traded to Duking who gave him a Geodude.

His next stop was Outskirt Stand and was challenged by Miror B. whose four Lombre fell to Nidoking's Megahorn, Nidoran F's Poison Fang then she evolved into Nidorina, Scolipede's Megahorn, and Shedinja's Leech Life while the Shadow Nosepass was poisoned by Meganium's Poison Powder, snagged, and then purified.

Then he received a Shadow Togepi from Hordel and was purified as well was traded to him and got and Elekid in exchange.

He went inside the Cipher Key Lair and was challenged by Cipher Peon Humah whose Seviper and Murkrow feel to Geodude's Double-Edge and Electrode's Zap Cannon. The Shadow Paras and Shadow Growlithe were burned by a Will-O-Wisp from Emboar and paralyzed by a Thunder Wave from Porygon-Z. Then Ash snagged and purified Paras and Growlithe.

Next came Cipher Peon Gorog whose Rhyhorn, Swalot, Golbat, and Sharpedo fell to Blastoise's Bubble Beam, a Bulldoze from Geodude who evolved in Graveler, Oricorio's Revelation Dance, and Raichu's Volt Tackle while the Shadow Shellder was poisoned by Muk's Toxic and was snagged then purified.

Then came was Cipher Peon Lok whose Furret and Togetic fell to Lucario's Brick Break and Bergmite's Avalanche while the Shadow Rufflet and Shadow Beedrill who were snagged and purified after being poisoned by a Toxic from Skrelp and Beedrill was put to sleep by a Grass Whistle from Sunflora.

After that was Cipher Peon Jelstin whose Roselia, Hoppip, and Bellossom fell to Psychic from Ralts who evolved into Kirlia, an Ice Ball from Spheal, and a Flamethrower from Salandit. While the Shadow Vikavolt was put to sleep by a Yawn from Komala. Ash then snagged and purified Vikavolt.

Fifth was Cipher Peon Targ whose Ninetales, Jumpluff, and Azumarill fell to Mantine's Bubble Beam, Vanillite's Ice Beam, and Elekid's Thunder Punch while the Shadow Tangela and Shadow Vivllon who had the extremely rare Poké Ball pattern were snagged then purified. After Tangela was put to sleep by Lapras' Sing and Vivillon was put to sleep by Paras' Spore.

Then he was challenged by Cipher Peon Snidle whose Shedinja, Wobbuffet, and Vibrava fell to Infernape's Fire Punch, Crawdaunt's Night Slash and a Blizzard from Vanillite who evolved into Vanillish while the Shadow Magneton was snagged then purified after being poisoned by Salandit's Toxic.

He was then challenged by Cipher Peon Angic whose Golduck, Hitmontop, and Hariyama fell to a Zap Cannon from Elekid who evolved into Electibuzz, a Sky Attack from Sigilyph, and a Psychic from Grumpig while the Shadow Venomoth and Shadow Weepinbell were snagged then purified after being paralyzed by a Thunder Wave from Nosepass and Magneton.

He was then challenged by Cipher Peon Smarton who Huntail, Cacturne, Weezing and Ursaring who fell to Magneton's Thunderbolt, Heracross' Megahorn, Venomoth's Psychic, and Medicham's High Jump Kick while the Shadow Arbok was snagged and purified after getting paralyzed by a Thunder Wave from Mismagius.

The last trainer for him to face was Cipher Admin Gorigan. His Lairon, Sealeo, Slowking, and Ursaring were defeated by Hawlucha's High Jump Kick, Hariyama's Brick Break, Krookodile's Crunch, and Electibuzz's Cross Chop. While the Shadow Combusken and Hypno were snagged and purified.

The next stop was Citadark Isle were he snagged these Shadow Pokemon. Shiinotic and Spinda from Cipher Peon Haben, Golduck and Sableye from Navigator Abson, Raticate and Dodrio from Chaser Furgey, Corsola and Indigo Core Minior from Sailor Golos, Oranguru and Seaking from Hunter Jetsal, Farfectch'd and Druddigon from Cipher Admin Lovrina, Chimecho and Araquanid from Cipher Peon Bastil, Kangaskhan and Banette from Cipher Peon Litnar, Magmar and Pinsir from Cipher Peon Grupel, Volbeat and Illumise from Chaser Nalix, Wobbuffet and Bewear from Hunter Ibran, Slowking and Pyukumuku from Cipher Peon Jargo, Lampent and Rapidash from Cipher Peon Kolest, Cacturne and Clawitzer from Cipher Peon Kolin, Sawk and Hitmonchan from Cipher Peon Karbon, Throh and Hitmonlee from Cipher Peon Petro, Tsareena and Vileplume from Cipher Peon Jaymi, Super Size Gourgeist and Golisopod from Cipher Peon Gromlet, Togedemaru and Lickitung from Cipher Peon Geftal, Scyther and Chansey from Cipher Peon Ledon, Starmie and Solrock from Cipher Admin Snattle, Mandibuzz; Drampa; Jynx; and Golurk from Cipher Admin Ardos, Poliwrath and Mr. Mime from Cipher Admin Gorigan, Crabominable and Dugtrio from Cipher Peon Kolax, Manectric; Salamence; Marowak; and Cryogonal from Cipher Admin Eldes, Malamar and Pangoro from Cipher RD Loket, and Barbaracle and Dhelmise from Cipher RD Kaller.

Also they were all purified.

He then approached Greevil when Shadow Lunala attacked so he sent out Rayquaza who constricted Lunala was snagged and purified but took a lot of effort while Shadow Rhydon, Landorus, Exeggutor, Tornadus, Bouffalaunt, and Thundurus were snagged and purified while Grand Master Greevil disbanded Cipher.

The last Shadow Pokémon was at Gateon Port where he challenged by Miror B. whose five Ludicolo fell to Dodrio's Drill Peck, Mandibuzz's Air Slash, Vikavolt's Air Slash, Salamence's Fly, and Aerodactyl's Sky Attack while Shadow Dragonite was snagged and purified.

Before he left he went to Oasis Poke Spot he caught a Shiny Magikarp, Shiny Feebas, and a Surskit which traded to Duking and received a Dwebble in exchange after that he went through a Hoopa-made portal back home.

 **Ash's Pokemon of Kanto/Orange Islands/Hall of Origin: Raichu, Venusaur, Charizard, Blastoise, Kingler, Primeape, Muk, Tauros, Snorlax, Articuno, Suicune, Lugia, Ho-Oh, Latias, Kyogre, Deoxys, Azelf, Heatran, Regigigas, Giratina, Darkrai, Victini, Cobalion, Terrakion, Virizion, Zekrom, Keldeo, Meloetta, Xerneas, Yveltal, Zygarde, Hoopa, Volcanion, Butterfree, Pidgeot, Lapras, Goodra, Lucario, Tyranitar, Florges, Wailord, Spiritomb, Hippowdon, Swampert, Sawsbuck, Abomasnow, Aurorus, Luxray, Trevenant, Froslass, Bastiodon, Omastar, Kabutops, Aerodactyl, Houndoom, Volcarona, Beheeyem, Vespiquen, Grumpig, Relicanth, Gardevoir, Durant, Aegislash, Jellicent, Zoroark, Cofagrigus, Sigilyph, Darmanitan, Unown, Flygon, Scolipede, Whimsicott, Latios, Rayquaza, Genesect,**

 **Ash's Pokemon of Johto: Heracross, Meganium, Typhlosion, Feraligatr, Noctowl, Donphan, Jolteon, Girafarig, Nidoking**

 **Ash's Pokemon of Hoenn: Swellow, Sceptile, Crawdaunt, Torkoal, Glalie**

 **Ash's Pokemon of Sinnoh: Staraptor, Torterra, Infernape, Floatzel, Gliscor, Garchomp**

 **Ash's Pokemon of Unova: Unfezant, Samurott, Emboar, Scrafty, Leavanny, Seismitoad, Gigalith, Krookodile**

 **Ash's Pokemon of Kalos: Greninja, Talonflame, Hawlucha, Noivern, Floette, Sylveon, Tyrantrum, Steelix, Cradily, Rampardos**

 **Ash's Pokemon of Orre: Espeon, Umbreon, Hariyama, Empoleon, Furret, Mismagius, Quagsire, Magcargo, Ninjask, Ampharos, Jumpluff, Yanmega, Octillery, Mantine, Qwilfish, Medicham, Altaria, Sudowoodo, Dedenne, Dunsparce, Hitmontop, Regirock, Ledian, Regice, Porygon-Z, Stantler, Mamoswine, Weavile, Ambipom, Honchkrow, Forretress, Ariados, Granbull, Kommo-o, Registeel, Delphox, Skarmory, Miltank, Absol, Flareon, Tropius, Metagross, Hydreigon, Armaldo, Delibird, Sunflora, Chesnaught, Smeargle, Ursaring, Shuckle, Togekiss, Vaporeon, Cubchoo, Shedinja, Poochyena, Litleo, Spheal, Baltoy, Stunfisk, Gulpin, Seedot, Mareanie, Numel, Dustox, Carvahna, Nidoran F, Zubat, Voltorb, Machoke, Meinfoo, Vulpix, Bellossom, Duskull, Ralts, Mawile, Bergmite, Masquerain, Clamperl, Vanillish, Fomantis, Brionne, Salandit, Skrelp, Oricorio, Komala, Natu, Roselia, Meowth, Koffing, Seel, Lunatone, Aron, Sandshrew, Graveler, Nosepass, Electibuzz, Zangoose, Paras, Growlithe, Shellder, Rufflet, Beedrill, Vikavolt, Tangela, Vivillon, Magneton, Venomoth, Weepinbell, Arbok, Combusken, Hypno, Shiinotic, Spinda, Golduck, Sableye, Raitcate, Dodrio, Corsola, Minior, Oranguru, Seaking, Farfetch'd, Druddigon, Chimecho, Araquanid, Kangakhan, Banette, Magmar, Pinsir, Volbeat, illumise, Wobbuffet, Bewear, Slowking, Pyukumuku, Lampent, Rapidash, Cacturne, Clawitzer, Sawk, Hitmonchan, Throh, Hitmonlee, Tsareena, Vileplume, Gourgeist, Golisopod, Togedemaru, Lickitung, Chansey, Scyther, Starmie, Solrock, Mandibuzz, Drampa, Jynx, Golurk, Poliwrath, Mr. Mime, Crabominable, Dugtrio, Manectric, Salamence, Marowak, Cryogonal, Malamar, Pangoro, Barbaracle, Dhelmise, Lunala, Rhydon, Landorus, Exeggutor, Bouffalaunt, Tornadus, Thundurus, Dragonite, Feebas, Magikarp, Dwebble**


End file.
